1 package jalview.io.gff;
5 public interface SequenceOntologyI
8 * selected commonly used values for quick reference
11 public static final String POLYPEPTIDE = "polypeptide";
14 public static final String PROTEIN_MATCH = "protein_match";
17 public static final String NUCLEOTIDE_MATCH = "nucleotide_match";
20 public static final String CDS = "CDS";
23 public static final String SEQUENCE_VARIANT = "sequence_variant";
26 public static final String EXON = "exon";
29 public static final String TRANSCRIPT = "transcript";
31 // SO:0001621 isA sequence_variant but used in Ensembl as a transcript
32 public static final String NMD_TRANSCRIPT_VARIANT = "NMD_transcript_variant";
35 public static final String GENE = "gene";
37 public boolean isA(String childTerm, String parentTerm);
40 * Returns a sorted list of all valid terms queried for (i.e. terms processed
41 * which were valid in the SO), using the friendly description.
43 * This can be used to check that any hard-coded stand-in for the full SO
44 * includes all the terms needed for correct processing.
48 public List<String> termsFound();
51 * Returns a sorted list of all invalid terms queried for (i.e. terms
52 * processed which were not found in the SO), using the friendly description.
54 * This can be used to report any 'non-compliance' in data, and/or to report
55 * valid terms missing from any hard-coded stand-in for the full SO.
59 public List<String> termsNotFound();